1. Revised usage to 80 chars
	2. GPL headers
	3. Added new stdin logic
	4. Changed logo.
	5. Revised the usage statement.

	1. Revised usage to 80 chars
	2. GPL headers
	3. Added new stdin logic
	4. Changed logo.
	5. Revised the usage statement.

	1. Revised usage to 80 chars
	2. GPL headers
	3. Added new stdin logic
	4. Changes logo.
	5. Revised the usage statement.

	1. Revised usage to 80 chars
	2. GPL headers
	3. Added new stdin logic
	4. Changes logo.
	5. Updated bedFile.cpp's loadBedIntoMapBin to support stdin.

	1. Revised usage to 80 chars
	2. GPL headers
	3. Added new stdin logic
	4. Changes logo.
	5. Updated bedFile.cpp's loadBedIntoMapNoBin.  Bug in stdin logic.

	1. Revised usage to 80 chars
	2. GPL headers
	3. Added new stdin logic

	1. Revised usage to 80 chars
	2. GPL headers
	3. Added new stdin logic

	1. Added GPLv2 license to entire distribution
	2. Added GPL headers to intersect and window
	3. Added new stdin logic to windowBed

	1. Got parseGffLine working
	2. Added GFF support to the reportBed* methods.
	3. Cleaned up the stdin / parsing logic and centralized it within bedFile.cpp.
	This removes some of the complexity from each of the tools and tidies the codebase
	overall.

	Not thoroughly tested but looks good so far.
	Initial cut at a GFF parser...needs work.

  Rewrote complementBed to use a slower but much simpler approach. This resolves several bugs with the previous logic.

   This becomes the new model for handling files/stdin,
   rather than duplicating the main logic of each porgram
   in a block for files and a block for stdin.

   Much slicker.

	Fixed a bug in subtractBed that prevent a file from subtracting itself when the following is used:
	$ subtractBed -a test.bed -b test.bed

	Fixed a bug in closestBed that caused all nearby (not just closest) features to be returned.

1

	Ready for publication release.
	Checked all of the help messages.
	Cleaned up some inconsistencies.

	Working on maskFastaFromBed, permuteBed and addFlanksBed

	Forced an exit if negative coordinates are encountered.

	1. Updated the mergeBed documentation to describe the -names option which allows one to report the names of the
	features that were merged (separated by semicolons).

   Changed windowBed to optionally define the left and right windows according to
   strandedness.

The memory usage is now less than 2.0 Gb.

	Fixed an obvious bug in subtractBed causing incorrect behavior when
	two features in B overlapped with a feature in A.

	This allows the names field from all merged intervals to be reported in the merged block.

=== Notable changes in this release ===
1.  coverageBed will optionally only count features in BED file A (e.g. sequencing reads) that overlap with
	the intervals/windows in BED file B.  This has been requested several times recently and facilitates CHiP-Seq and
	RNA-Seq experiments.

2.  intersectBed can now require a minimum __reciprocal__ overlap between intervals in BED A and BED B.  For example,
	previously, if one used -f 0.90, it required that a feature in B overlap 90% of the feature in A for the "hit"
	to be reported.  If one adds the -r (reciprocal) option, the hit must also cover 90% of the feature in B.  This helps
	to exclude overlaps between say small features in A and large features in B:

	A ==========
	B  **********************************************************

	-f 0.50 (Reported), whereas -f 0.50 -r (Not reported)

3.  The score field has been changed to be a string.  While this deviates from the UCSC definition, it allows one to track
	much more meaningful information about a feature/interval.  For example, score could now be:

	7.31E-05  (a p-value)
	0.334577  (mean enrichment)
	2:2.2:40:2 (several values encoded in a string)

4.  closestBed now, by default, reports __all__ intervals in B that overlap equally with an interval in A.  Previously, it
	merely reported the first such feature that appeared in B.  Here's a cartoon explaining the difference.

	**Prior behavior**

	A	 ==============
	B.1        				++++++++++++++
	B.2       				++++++++++++++
	B.3               				+++++++++

	-----------------------------------------
	Result = B.1 			++++++++++++++

	**Current behavior**

	A	 ==============
	B.1        				++++++++++++++
	B.2       				++++++++++++++
	B.3               				+++++++++

	-----------------------------------------
	Result = B.1 			++++++++++++++
			 B.2 			++++++++++++++

	Using the -t option, one can also choose to report either the first or the last entry in B in the event of a tie.

5.  Several other minor changes to the algorithms have been made to increase speed a bit.